rs647861

Variant names:

• chr17-77259879-T-C
• rs647861
• ENST00000581657.1:n.138-1531A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000581657.1(SEPTIN9-DT):​n.138-1531A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,824 control chromosomes in the GnomAD database, including 42,341 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42341 hom., cov: 29)
• Consequence: SEPTIN9-DT ENST00000581657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

Genes affected

SEPTIN9-DT (HGNC:52818): (SEPTIN9 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEPTIN9-DT	ENST00000581657.1	n.138-1531A>G		intron_variant	Intron 1 of 1	3
SEPTIN9-DT	ENST00000701682.1	n.595-1531A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112753 AN: 151706 Hom.: 42310 Cov.: 29

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.755

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.743 AC: 112830 AN: 151824 Hom.: 42341 Cov.: 29 AF XY: 0.736 AC XY: 54581 AN XY: 74190

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.748

Alfa AF: 0.743 Hom.: 49788

Bravo AF: 0.751

Asia WGS AF: 0.592 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs647861; hg19: chr17-75255961;